If you are running MyPet-NPC too you can delete that now as it is included into MyPet itself.
If you never touched the skilltrees you can skip this step!
If you made your own skilltrees or edited the default ones you need to convert them to the new format using the following steps:
open up the new SkilltreeCreator
select the folder you want to save your new skilltrees in
your browser will open and you will see the new Skilltree Creator​
open the menu on the top left hand corner
select Import Legacy Skilltree
follow the 3 steps of the wizard
hit the save button
upload the new .st.json
files to the skilltrees folder on your server
MyPet doesn't support numeric item IDs anymore. All settings that requires an config item will require the 1.13 item ID even if you don't run a 1.13 server